Abstract
This paper gives a subjective look at the high performance computing from the computational chemistry perspective. Using basic ab initio and molecular dynamics algorithms as examples of typical computational chemistry problems, the software engineering and architectural issues of contemporary high performance computers are discussed. The parallel computational chemistry is also presented, with a brief discussion of distributed environments used.
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Hehre, W. J., Radom, L., Rague Schlayer, P. von, and Pople, J. A. Ab Initio Molecular Orbital Theory. John Wiley & Sons, New York, 1986.
Foresman, J. B. and Frisch, Æ. Exploring Chemistry with Electronic Structure Methods. Gaussian, Inc., Pittsburgh, PA, second edition, 1996.
Lybrand, T. P. Computer simulation of biomolecular systems using molecular dynamics and free energy perturbation methods. In Lipkowitz, K. B. and Boyd, D. B., editors, Reviews In Computational Chemistry, volume I, pages 295–320, New York, 1990. VCH Publishers, Inc.
Frisch, M. J., Trucks, G. W., Schlegel, H. B., Gill, P. M. W., Johnosn, B. G., Robb, M. A., Cheeseman, J. R., Keith, T., Petersson, G. A., Montgomery, J. A., Raghavachari, K., Cioslowski, J., Stefanov, B. B., Nanayakkara, A., Challacombe, M., Peng, C. Y., Ayala, P. Y., Chen, W., Wong, M. W., Andres, J. L., Binkley, J. S., Defrees, D. J., Baker, J., Stewart, J. P., Head-Gordon, M., Gonzales, C., and Pople, J. A. Gaussian 94, Revision C.3. Gaussian, Inc., Pittsburgh, PA, 1995.
Frisch, M. J., Frisch, Æ., and Foresman, J. B. Gaussian 94 Programmer's Reference. Gaussian, Inc., Pittsburgh, PA, 1994.
Dowd, K. High Performance Computing. O'Reilly and Associates, Inc., Sebastopol, CA, 1993.
Lenoski, D. E. and Weber, W.-D. Scalable Shared-Memory Multiprocessing. Morgan Kaufmann Publishers, Inc., San Francisco, CA, 1995.
Fosdick, L. D., Jessup, E. R., Schaube, C. J. C., and Dominik, G. An Introduction to High-Performance Scientific Computing, chapter 11–14, pages 335–530. The MIT Press, Cambridge, MA, 1995.
Laganà, A., Gervasi, O., Baragli, R., Laforenza, D., and Perero, R. Where are embarassingly parallel problems? The atom-diatom quasiclassical reactivity. Theoretica Chimica Acta, 84:413–422, 1993.
Kendall, R. A., Harrison, R. J., Littlefield, R. J., and Guest, M. F. High performance computing in computational chemistry: Methods and machines. In Lipkowitz, K. B. and Boyd, D. B., editors, Reviews In Computational Chemistry, volume VI, pages 209–316, New York, 1995. VCH Publishers, Inc.
Geist, G. A., Beguelin, A., Dongarra, J. J., Jiang, W., Manchek, R., and Sunderam, V. S. PVM: A User's Guide and Tutorial for Networked Parallel Computing. The MIT Press, Cambridge, MA, 1994.
Harrison, R. J. Portable tools and applications for parallel computers. Int. J. Quant. Chem., 40:847, 1991. TCGMSG available from ftp.tcg.anl.gov.
Carriero, N. and Gelernter, D. How to write parallel programs: A First Course. The MIT Press, Cambridge, MA, 1990.
Dongarra, J., Gengler, M., Tourancheau, B., and Vigoroux, X., editors. EuroPVM'95, Paris, 1995. Hermès.
Dongarra, J. J., Madsen, K., and Wasniewski, J., editors. Applied Parallel Computing, Heidelberg, 1995. Springer Verlag.
Liddell, H., Colbook, A., Hertzberger, B., and Sloot, P., editors. High-Performance Computing and Networking, Heidelberg, 1996. Springer Verlag.
Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. S., III, T. E. C., Ferguson, D. M., Seibel, G. L., Singh, U. C., Weiner, P. K. Weiner, and Kollman, P. A. Amber 4.1. Technical report, University of California, San Francisco, 1995.
Smith, W. Molecular dynamics on distributed memory (MIMD) parallel computers. Theoretica Chimica Acta, 84:385–398, 1993.
Sterling, T. L., Messina, P. C., and Smith, P. H. Enabling Technologies for Petaflops Computing. The MIT Press, Cambridge, MA, 1994.
Integrating Fault Tolerance in off-the-shelf Massively Parallel Systems, Brussels, 1996. ESPRIT Workshop within HPCN Europe'96.
Lamotte, J.-L. A tool for the numerical validation of parallel code programming with Fortran 77 and PVM. In Dongarra et al. [14], pages 173–178.
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Matyska, L. (1996). High performance computing — The computational chemistry perspective. In: Jeffery, K.G., Král, J., Bartošek, M. (eds) SOFSEM'96: Theory and Practice of Informatics. SOFSEM 1996. Lecture Notes in Computer Science, vol 1175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/BFb0037405
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DOI: https://doi.org/10.1007/BFb0037405
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